Hey Vince,
I had started testing a version that will create pop-up automatically, but I paused because there were many rough edges around when should popup really show. We need to answer question like what to do with site wide notes: do you show them for each URL change, or just once. You can close the pop-up and make sure it doesn't show until that page reloads, but does it really make sense to minimize -- if you want to pull up and see the notes again, you can always do that by just clicking the extension button. Also, do you want to have dragging capability (that will make things more complex, of course).
I need to think of the design more carefully. I'll restart the work on this soon.
Cheers,
Manu